In metazoans, gene expression is regulated in a tissue/cell-type specific manner predominantly via stretches of noncoding sequence referred to as cis regulatory modules (CRMs) that regulate the expression of (typically) the adjacent gene(s). CRMs contain 1 or more DNA binding sites for 1 or more sequence-specific, regulatory transcription factors (TFs) that function to activate or repress the expression of target gene(s); CRMs that activate gene expression are frequently referred to as transcriptional ?enhancers?, while those that repress gene expression are referred to as ?silencers?. The goals of this renewal project are to extend our ?enhancer-FACS-Seq? (eFS) technologies for high-throughput experimental assays to analyze additional functional features of tissue/cell-type-specific CRMs in vivo in whole Drosophila embryos in a genomic context, and to use them to identify cis regulatory codes that control gene expression in a tissue- and cell-type-specific manner. We will focus on the developing embryonic somatic mesoderm in Drosophila as our model system. We anticipate that our approaches and data should be applicable to other systems and organisms, including human.